At the end of Prometheus, the alien that Elizabeth Shaw extracted from her womb kills the Engineer. Later on, a primary form of alien xenomorph is seen bursting out of the Engineer's chest. The scene takes place in Meredith Vickers' escape pod, stranded at a distance from the Engineers' crashed ship.

At the beginning of Alien, the team that explores the derelict ship discovers the body of an Engineer pilot:

The corpse wears what we now know is some sort of armor, and his chest has been damaged by an alien xenomorph, as we later figure out.

Everything seems to indicate that the corpse in Alien is actually the Engineer in Prometheus. However, there are two major discrepancies:

The Engineer is killed in the escape pod, not in his pilot seat.

The corpse in Alien is much taller than the Engineer in Prometheus.

What other theory could possibly explain how a (much taller) Engineer sat in the crashed ship and was killed by a xenomorph?

We're looking for long answers that provide some explanation and context. Don't just give a one-line answer; explain why your answer is right, ideally with citations. Answers that don't include explanations may be removed.

5 Answers
5

Prometheus and Alien deliberately share a lot of themes, as well as the same universe, but they are not directly prequel and sequel (spoilers follow...)

The Space Jockey in Alien is old enough to be fossilised. Possibly by the same events that wiped out the Engineers in Prometheus (2000 years ago according to Shaw's carbon dating) but too close to Alien's dates to be the same one.

The planets have different names: LV-223 in Prometheus and LV-426 in Alien.

The planets have different atmospheres - LV-426 is "primordial" while LV-223 is "almost breathable" except for the too high CO2, which is not the case in the pyramids.

There are no alien structures on LV-426.

The ship in Prometheus is carrying black goo vases, but no eggs. The one in Alien lots of identical eggs, but no black goo.

So what is the same?

The Space Jockey in Alien is a giant 'human' in a suit.

The black goo is the source of both the alien in Alien and the various things in Prometheus. The DNA of its victim species has some effect on the result, and the final result in Prometheus is approaching the alien from Alien.

The eggs being carried by the crashed ship in Alien are probably the result of the black goo on something other than human, maybe something that layed eggs instead of giving birth.

I think that the ship in Alien is another attempt to wage biological warfare by the space jockeys/engineers. Either the eggs are before or after the black goo - both obviously went wrong so it's hard to guess which attempt came first.

The space jockeys/engineers share humanity's propensity for building really stupid ways to kill each other, as well as our DNA.

Ridley Scott has said that he envisions Prometheus as a trilogy, so maybe this gets tied up somehow.

The moon visited by the Prometheus, called LV-223, is not the same planet visited by the Nostromo in Alien, which is called LV-426. I believe that the latter was not named on screen until the second film, Aliens. So they are two different Engineer ships and two different dead Engineers.

Similarly, the distress call/warning intercepted by the Nostromo was in an alien language and needed to be decrypted, so it was not the warning in English sent by the humans in Prometheus.

+1: Interesting answer. But the ship in Alien is stranded in a very similar position as in Prometheus. Also, are we sure Aliens takes place on the same planet as Alien?
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Laurent PireynJun 4 '12 at 16:35

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I'm pretty sure it is. See scenes 9 and 10 of this Aliens screenplay where it's mentioned that, since the events of Alien, LV-426 has been colonised and renamed Acheron.
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DeditosJun 4 '12 at 18:11

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I haven't read the question fully in order to avoid spoilers, however, I will just add that Ridley Scott has stated (on BBC Five Live's film programme) there may be two sequels to Prometheus that fill in the gap between it and Alien. Or to put it another way, he has the entire story arc planned out and it is two films worth.
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DisgruntledGoatJun 4 '12 at 20:45

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@DisgruntledGoat Thanks for the heads up. I've just listened to that interview and in it Scott also states that LV-223 and LV-426 are definitely not the same planet.
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DeditosJun 4 '12 at 21:55

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@LaurentPireyn - It is stated quite clearly in Aliens that it's the same planet as that in Alien. When Ripley tells them that the crashed ship was on LV-426, the corporate guy tells her that the colonists who've been living there for decades haven't complained about any hostile alien life forms. He then ordered a survey mission to the grid coordinates that Ripley provided, and the family they sent found the same crashed ship.
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David HarknessSep 15 '12 at 23:38

Ridley Scott has stated clearly before this movie was released that it is not a prequel to the Alien film. It takes place almost a hundred years before LV-426 is found.

With that said, Ridley Scott has talked about making a trilogy of the Prometheus films. We can assume that the strange looking xenomorph shown at the end of Prometheus is an early ancestor to the xenomorph shown in Alien.

Is this the mother to all aliens or just an example of a xenomorph hatched from an Engineer?

There is no actual evidence that Prometheus takes place on a different planet. There is a widely accepted "theory" that it takes place on LV-223 instead of the LV-426, but there is no hard evidence, other than word of mouth. Even if that is from the director himself; it's still word of mouth. The truth is: they screwed up on the continuity either on purpose (just to add one last scare), or on accident (just to add one last scare)--and LV-223 was just a way for fans to cope with the continuity error . . . which it is.

The reason why the atmosphere changed from Prometheus to Alien is because the spaceship which is in itself a terraforming mechanism crashed and hence, wasn't working properly. What happens when an oxygen super producing underground spaceship stops working? The area around it has becomes less full of oxygen. Without plantlife on earth, earth would have mor Carbon Dioxide in the air . . . and it's the same with Prometheus. The ship no longer produced oxygen and thus more carbon dioxide in the air many years in the future when the people from Alien landed on the planet (and the spaceship is in the exact same position, mind you).

And, likewise, the reason why there were no eggs in the fallen spaceship in Prometheus is because the alien that popped out of the super human's chest hadn't yet laid the eggs.

It's really quite obvious that Prometheus and Alien takes place on the same planet; or at least the writers wrote it for that reason because all the pieces of the puzzle seem to fit the same way The Thing prequel fit with the events in original The Thing.

In conclusion, it being a different planet was only born to cope with this particular continuity error . . . and it is a continuity error. A BIG ONE. Such a big one that perhaps they (being perhaps Ridley Scott) would purposefully plant it.

In the movie it says LV-223 on the computer screen of the Prometheus! That is not a theory it is printed in green and white, not LV-426. Sounds like there is plenty of opportunities to get from here to there if there are 2 more movies.
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user1463Jun 9 '12 at 5:33

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It's a widely accepted "theory" that it takes place on LV-223 instead of LV-426 because that's what is stated on screen.
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user209Jun 10 '12 at 3:35

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You say there's no evidence that they're different planets. There's even less evidence that they're the same planet. The only similarity between the two worlds is that both have a crashed space jockey ship on them. The ships have different cargos, one has a chest-burst space jockey in it, the other a dead octogenarian billionare and a company-built escape pod crashed next to it. What makes you think they're the same planet?
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KeithJun 12 '12 at 12:05

Downvote because it is not at all "obvious" as the comment above neatly explains.
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Shiz Z.Jun 16 '12 at 16:08

-1 because there is zero evidence that they are the same planet and plenty of evidence across three movies that they are different planets.
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David HarknessSep 15 '12 at 23:46